Preface xv
About the Authors xvii
About the Companion Website xviii
Part I: Unity 3
1 Microbial Phylogeny—The Three Domains of Life 5
Introduction 6
The Three Branches of Life: Bacteria, Archaea, and Eukarya 6
The 16S/18S rRNA Gene as a Basis for Phylogenetic Comparisons 7
The Modern Molecular Phylogenetic Tree of Life 12
Phylogenetics and Earth History 14
2 Metabolic Unity—Generation of Biosynthetic Precursors 21
Making Connections 22
The Purpose of Central Metabolism 22
The 12 Essential Precursors 23
The Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25
Structure and Energy Exchange of Key Coenzymes 28
Controlling the Direction of Carbon Flow during Glycolysis 29
The Pentose Phosphate Pathway (PPP) 31
The Entner-Doudoroff (ED) Pathway 33
The Transition Reaction: Carbon Flow into the Tricarboxylic Acid (TCA) Cycle 36
The Tricarboxylic Acid (TCA) Cycle 37
Anaplerotic Reactions 37
The Branched or Incomplete Tricarboxylic Acid (TCA) Pathway 41
The Glyoxylate Cycle 41
Reversing Carbon Flow from the Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway 43
3 Cellular Components—What’s In a Cell 51
Making Connections 52
Estimating Molecular Concentrations 52
Physiologically Relevant Protein Concentrations 54
Measuring Enzyme Activity: Basic Principles of Enzyme Assays 55
Michaelis-Menten Kinetics 58
Studying the Proteome 59
The Physiological Role and Composition of Cellular RNA 61
The Physiological Role and Composition of Cellular DNA 63
Studying the Genome and the Transcriptome 64
4 Cellular Growth 73
Making Connections 74
Methods to Monitor Bacterial Growth 74
The Phases of Bacterial Growth in Batch Culture 78
Requirements for Microbial Growth 80
Diauxic Growth 80
Exponential Growth Kinetics 81
Chemostats 83
Characteristics of Stationary-Phase Cells 84
Proteins Important for Cell Shape and Cell Division 85
Chromosome Segregation 86
5 Bioenergetics and the Proton Motive Force 95
Making Connections 96
Cellular Mechanisms for ATP Synthesis 96
Chemiosmotic Theory 98
ATP Synthase 99
The Proton Motive Force (PMF) 99
Quantifying the Proton Motive Force 99
Cellular Proton Levels 100
Environmental Impacts on the Proton Motive Force (PMF) 100
Experimentally Measuring the Proton Motive Force (PMF) 101
6 Respiration and Fermentation 107
Making Connections 108
The Basic Components of an Electron Transport Chain (ETC) 108
Electrode/Reduction Potential (E0′) 109
Brief Review of the Electron Transport Chain (ETC) in Mitochondria 110
Q Cycle of Mitochondria 113
Bacterial Electron Transport Chains (ETCs) 113
Q Loop of Bacteria 115
Electron Donors and Acceptors in Bacteria 115
Fermentation 117
7 Regulation—Posttranslational Control 127
Making Connections 128
Importance of Regulatory Processes 128
Allosteric Regulation of Enzymes 129
Allosteric Regulation of Branched Pathways 131
Covalent Modifications 134
Posttranslational Regulation in the Sugar Phosphotransferase System (PTS) 138
8 Gene Regulation—Transcription Initiation and Posttranscriptional Control 147
Making Connections 148
Transcription Terminology 148
Bacterial Transcription Initiation and Elongation 149
Bacterial Transcription Termination 151
Regulatory cis- and trans-Acting Elements Impacting Transcription 153
Examples of Different Promoter Structures 154
Transcriptional Regulation of the lac Operon 156
Activation and Repression by the Global Regulator Cra 158
Attenuation 158
Posttranscriptional Regulation 161
Methods Used to Study Gene Regulation 163
Methods to Demonstrate Protein–DNA Interactions 164
Interlude: From Unity to Diversity 177
Metabolic Diversity 178
Global Nutrient Cycles 179
Structural and Regulatory Diversity of Microbes 180
Part II: Diversity 183
9 Autotrophy 185
Making Connections 186
Autotrophy 186
Calvin Cycle 187
Reductive Tricarboxylic Acid (rTCA) Cycle 191
Reductive Acetyl-CoA Pathway 193
3-Hydroxypropionate (3HP) Bi-cycle 195
3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195
Why So Many CO2 Fixation Pathways? 197
10 Phototrophy 207
Making Connections 208
Phototrophy 208
Chlorophyll-Based Phototrophy 209
Cellular Structures Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and Unique Membrane Organizations 211
Oxygenic Photoautotrophy in the Cyanobacteria 215
Anaerobic Anoxygenic Phototrophy in the Phototrophic Purple Sulfur and Purple Nonsulfur Bacteria 218
Anaerobic Anoxygenic Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green Nonsulfur Bacteria, Respectively) 221
Anaerobic Anoxygenic Photoheterotrophy in the Firmicutes 224
Aerobic Anoxygenic Phototrophy 224
Retinal-Based Phototrophy 225
11 Chemotrophy in the Carbon and Sulfur Cycles 233
Making Connections 234
The Carbon Cycle 234
The Chemoorganotrophic Degradation of Polymers 236
The Chemoorganotrophic Degradation of Aromatic Acids 236
Chemoorganotrophy in Escherichia coli 241
Chemolithoautotrophy 246
Chemolithoautotrophy in Methanogens 248
Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251
One-Carbon (C1) Chemolithotrophy in Acetogens 253
The Sulfur Cycle 256
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate Reducers 256
Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259
The Anaerobic Food Web and Syntrophy 261
12 Microbial Contributions to the Nitrogen Cycle 275
Making Connections 276
Overview of the Nitrogen Cycle 276
Nitrogen Fixation 277
Biochemistry of Nitrogen Fixation 278
Regulation of Nitrogen Fixation 280
Symbiotic Plant-Microbe Interactions during Nitrogen Fixation 282
Assimilatory Nitrate Reduction 284
Ammonia Assimilation into Cellular Biomass 285
Nitrification: Ammonia Oxidation, Nitrite Oxidation, and Comammox 287
Anammox: Anaerobic Ammonia Oxidation 290
Denitrification 293
13 Structure and Function of the Cell Envelope 303
Making Connections 304
Fundamental Structure of the Cytoplasmic Membrane 304
Variation in Cytoplasmic Membranes 306
Transport across Cytoplasmic Membranes 306
Cell Wall Structures 311
Gram-Negative Outer Membrane 315
Periplasm 320
Additional Extracellular Layers 321
14 Transport and Localization of Proteins and Cell Envelope Macromolecules 333
Making Connections 334
Introduction to Cytoplasmic Membrane Protein Transport Systems 334
Secretory (Sec)-Dependent Protein Transport System 334
The Secretory (Sec)-Dependent Protein Transport Process 337
Signal Recognition Particle (SRP)-Dependent Protein Transport Process 338
Twin-Arginine Translocation (Tat) Protein Transport Process 339
Integration of Cytoplasmic Membrane Proteins 340
Gram-Negative Bacterial Outer Membrane Protein Secretion Systems 341
Secretory (Sec)- and Twin-Arginine Translocation (Tat)-Dependent Protein Secretion Systems 341
Secretory (Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343
Importance of Disulfide Bonds 347
Transport and Localization of Other Cell Envelope Components 348
15 Microbial Motility and Chemotaxis 363
Making Connections 364
Motility in Microorganisms 364
Bacterial Flagella and Swimming Motility 364
Regulation of Flagellar Synthesis in Escherichia coli 367
Mechanism of Swimming Motility 369
Archaeal Flagella 370
Bacterial Surface Motility 371
Chemotaxis 372
Conservation and Variation in Chemotaxis Systems among Bacteria and Archaea 380
Methods to Study Bacterial Motility and Chemotaxis 381
16 Quorum Sensing 389
Making Connections 390
Fundamentals of Quorum Sensing 390
Quorum Sensing and Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391
Basic Model of Quorum Sensing in Gram-Negative Proteobacteria 395
Basic Model of Quorum Sensing in Gram-Positive Bacteria 398
Interspecies Communication: the LuxS System 400
Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae 400
Quorum Quenching 402
17 Stress Responses 415
Making Connections 416
Oxidative Stress 416
Heat Shock Response 419
Sporulation 420
18 Lifestyles Involving Bacterial Differentiation 441
Making Connections 442
A Simple Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443
Differentiation in Filamentous Cyanobacterial Species 444
Life Cycle of Filamentous Spore-Forming Streptomyces: An Example of Bacterial Multicellularity 447
Life Cycle of Myxobacteria: Predatory Spore-Forming Social Bacteria 449
Biofilms: The Typical State of Microorganisms in the Environment 452
Index 467
